Reciprocal molecular markers were developed to distinguish the closely related parasitoid genera Encyrtus Latreille, Metaphycus Mercet and Paraceraptrocerus  Girault (Hymenoptera : Encyrtidae). These parasitoids are widely used in the biological control of soft scales and based upon morphology, it is extremely difficult to distinguish them. DNA extraction and RAPD-PCR were used to assess the amount of genetic variation within and among species at this locus. From parsimony analysis, populations of Encyrtus inflelix (Embleton), Metaphycus anneckei Guerrieri & Noyes and Paraceraptrocerus africanus Giralut were separated. Specific DNA markers of E. inflelix, P. africanus and M. anneckei at M.W. of (475.07, 429.60, 311.37bp < /em>) and (473.33bp), (700.0, 400.0 and 270.59bp < /em>) and, (918.79, 814.45, 771.44bp < /em>) for (AC07), (AE02), (B10) and (B07) primers, respectively were used.  Based upon the sequence variation among species, the present study appeared a simple molecular assay to rapidly and unambiguously distinguish E. inflelix, P. africanus and M. anneckei species.